Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A2 F1 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,081,402	G→A	T78T (ACC→ACT)	tktA ←	transketolase 1, thiamine triphosphate‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,081,402	0	G	A	100.0%	22.3 / NA	8	T78T (ACC→ACT)	tktA	transketolase 1, thiamine triphosphate‑binding
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (3/5); total (3/5)

ATACCCTGACCCAGCGGACCGGTGGTGGTTTCCACACCAGCGGTGTAACCCACTTCCGGGTGACCCGGAGTTTTAGAGTGCAGCTGACGGAAGTTTTTCAGTTCTTCCATCGGCAGATCGTAACCGGTGAGGTGCAGCAGGCTGTAGATCAGCATGGAGCCGTGGCCGTTGGACAGCACGAAGCGGTCACGGTCAGCCCAGGACGGATTCTGCGGGTTGTGTTTCAGGAAATCACGCCACAGGACTTCGGCAATGTCAGC  >  NC_000913/3081277‑3081536

aTACCCTGACCCAGCGGACCGGTGGTGGTTTCCACACCAGCGGTGTAACCCACTTCCGGGTGACCCGGAGTTTTAGAGTGCAGCTGACGGAAGTTTTTCAGTTCTTCCATCGGCAGATCGTAACCAGTGAGGTgcagca                                                                                                                           <  2:48932/139‑1 (MQ=255)

          ccAGCGGACCGGTGGTGGTTTCCACACCAGCGGTGTAACCCACTTCCGGGTGACCCGGAGTTTTAGAGTGCAGCTGACGGAAGTTTTTCAGTTCTTCCATCGGCAGATCGTAACCAGTGAGGTGCAGCAGGCTGTAGAt                                                                                                                 <  2:288525/139‑1 (MQ=255)

            aGCGGACCGGTGGTGGTTTCCACACCAGCGGTGTAACCCACTTCCGGGTGACCCGGAGTTTTAGAGTGCAGCTGACGGAAGTTTTTCAGTTCTTCCATCGGCAGATCGTAACCAGTGAGGTGCAGCAGGCTGTAGATCa                                                                                                               <  2:242405/139‑1 (MQ=255)

             gCGGACCGGTGGTGGTTTCCACACCAGCGGTGTAACCCACTTCCGGGTGACCCGGAGTTTTAGAGTGCAGCTGACGGAAGTTTTTCAGTTCTTCCATCGGCAGATCGTAACCAGTGAGGTGCAGCAGGCTGTAGATCAg                                                                                                              >  2:391532/1‑139 (MQ=255)

                      tggtggtTACCACACCAGCGGTGTAACCCACTTCCGGGTGACCCGGAGTTTTAGAGTGCAGCTGACGGAAGTTTTTCAGTTCTTCCATCGGCAGATCGTAACCAGTGAGGTGCAGCAGGCTGTAGATCAGCATGGAGcc                                                                                                     >  2:427944/1‑139 (MQ=255)

                                                          ggTGACCCGGAGTTTTAGAGTGCAGCTGACGGAAGTTTTTCAGTTCTTCCATCGGCAGATCGTAACCAGTGAGGTGCAGCAGGCTGTAGATCAGCATGGAGCCGTGGCCGTTGGACAGCACGAAGCGGTCACGGTCAGc                                                                 >  2:549837/1‑139 (MQ=255)

                                                                                               tttCAGTTCTTCCATCGGCAGATCGTAACCAGTGAGGTGCAGCTGGCTGTAGATCAGCATGGAGCCGTGGCCGTTGGACAGCACGAAGCGGTCACGGTCAGCCCAGGACGGATTCTGCGGGTTGTGTTTCAGGAAATCa                            <  1:427944/139‑1 (MQ=255)

                                                                                                                         aaCCAGTGAGGTGCAGCAGGCTGTAGATCAGCATGGAGCCGTGGCCGTTGGACAGCACGAAGCGGTCACGGTCAGCCCAGGACGGATTCTGCGGGTTGTGTTTCAGGAAATCACGCCACAGGACTTCGGCAATGTCAGc  <  1:549837/139‑1 (MQ=255)

ATACCCTGACCCAGCGGACCGGTGGTGGTTTCCACACCAGCGGTGTAACCCACTTCCGGGTGACCCGGAGTTTTAGAGTGCAGCTGACGGAAGTTTTTCAGTTCTTCCATCGGCAGATCGTAACCGGTGAGGTGCAGCAGGCTGTAGATCAGCATGGAGCCGTGGCCGTTGGACAGCACGAAGCGGTCACGGTCAGCCCAGGACGGATTCTGCGGGTTGTGTTTCAGGAAATCACGCCACAGGACTTCGGCAATGTCAGC  >  NC_000913/3081277‑3081536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A